How to batch join a sequence of images with a sequence of alphas?
What you try to achieve is extremely simple:
Just plug the RGB image to the Composite's node "Image" socket and plug the Alpha image to the alpha channel, and make sure you're saving to an unassociated alpha format, as PNG.
The same effect is achieved by just plugging a set alpha node and connect the output (Now RGBA with the new alpha assigned) to the Composite's "Image" socket.

Keep in mind that both methods will produce exactly what you want, but you won't be able to see it in the viewer, as Blender expects an associated buffer to display. The saved PNG will be fine.

That being said, it's important to remember that PNG and unassociated alpha are no the best choice for CG and VFX.
Associated alpha allows you to create composites where your transparent pixels can also be luminous, producing lighting effects that are absolutely impossible using unassociated (straight) alpha.
Preserving RGB is only useful when you want to do associated alpha compositing. It is completely useless with unassociated as the alpha over operation will make any pixel with alpha=0 disappear.